Contents

write_airr

Write an AIRR TSV

Description

write_airr writes a TSV containing AIRR formatted records.

Usage

write_airr(data, file, base = c("1", "0"), schema = RearrangementSchema, ...)

write_rearrangement(data, file, base = c("1", "0"), ...)

write_alignment(data, file, base = c("1", "0"), ...)

Arguments

data

data.frame of Rearrangement data.

file

output file name.

base

starting index for positional fields in the output file. Fields in the input data are assumed to be 1-based closed-intervals (R style). If "1", then these fields will not be modified. If "0", then fields ending in _start and _end will be converted to 0-based half-open intervals (python style) in the output file.

schema

Schema object defining the output format.

…

additional arguments to pass to write_delim.

Details

write_rearrangement writes a data.frame containing AIRR Rearrangement data to TSV.

write_alignment writes a data.frame containing AIRR Alignment data to TSV.

Examples

# Get path to the rearrangement-example file
file <- system.file("extdata", "rearrangement-example.tsv.gz", package="airr")

# Load data file
df <- read_rearrangement(file)

# Write a Rearrangement data file
outfile <- file.path(tempdir(), "output.tsv")
write_rearrangement(df, outfile)

See also

See Schema for the AIRR schema object definition. See read_airr for reading to AIRR files.

read_airr validate_airr